The intestinal epithelium is one of the most rapidly renewing tissues in the body, and thus the ideal tissue to study somatic stem and progenitor cell biology. The small intestinal epithelium is composed of a single layer of cells that contains four major differentiated cell types as well as intestinal stem cells (ISCs) and progenitor r transit amplifying cells that replenish differentiated cells throughout life. While the past twent years have seen great progress in our understanding of the signaling pathways and transcriptional regulators that control intestinal proliferation and differentiation, our understanding of the epigenetic factors that control these important processes is rather limited. To address this knowledge gap, I propose the following three interrelated yet independent Specific Aims: In specific Aim 1, we will determine the genome-wide atlas of epigenetic modifications of Lgr5-positive stem cells, transit amplifying or progenitor cells, and mature epithelial cells. We will perform integrative data analyses to identify the gene sets that are regulated by epigenetic modifications as the cells progress from stem to differentiated epithelial cell. In Aim 2, we will delineate the role of maintenance DNA methylation in intestinal stem cell renewal and epithelial differentiation, through conditional gene ablation of the maintenance DNA methylase Dnmt1. In Aim 3, we will test the hypothesis that the repressive H3K27me3 mark must be removed by the histone demethylase Jmjd3 in order to allow differentiation of intestinal epithelial cells, using inducible gene deletion. PUBLIC HEALTH RELEVANCE: Gastrointestinal cancer is a significant health problem, ranking fourth in incidence and second in death among cancers in the United States. Abnormal differentiation and increased proliferation of the intestinal epithelium are hallmarks of carcinogenesis. The molecular mechanisms that regulate cellular proliferation and differentiation in gastrointestinal development are far from being understood completely. Therefore, we will analyze the epigenomic regulation of intestinal stem cells, progenitor cells, and differentiated cells on the genome-wide level, and test the contribution of DNA methylation and histone demethylation to intestinal health.